Background/Disease: During the 14th century, a disease known as the bubonic plague wiped out about one-third of the population in Europe. Classified as a zoonotic disease, it spread to the human population by small rodents and their fleas. Also known as the Black Death, the disease killed an infected individual within 4 days if left untreated. People with the disease experienced swollen lymph nodes (buboes), chills, high fever, muscle cramps, seizures, and change in skin color. The swollen lymph nodes were commonly found in the armpits, groin or neck, and were associated with pain. The cause of the bubonic plague was recently confirmed to the organism Yersinia pestis. It is a gram-negative bacteria that can take three main forms, the bubonic plague being the most prominent. Yersinia pestis attacks humans by using organisms like a flea as a vector. The bacteria accumulates inside the gut of a flea, and once the flea bites a human host, infected blood from the flea enters a human. The bacteria quickly spreads to the lymph nodes, infecting the lymphatic system. Phagocytes are not effective against Yersinia pestis because the bacteria can resist phagocytosis and kill them instead. As the disease progresses, lymph nodes can become necrotic and problems with the lungs can occur. Over 200 different rodents and species can also serve as hosts even though the flea is the most common. Although the disease is not extremely present in humans as it once was 7 centuries ago, cases of the plague are still reported to the World Health Organization.
http://www.medicalnewstoday.com/articles/233648.php
Organism: Yersinia pestis YopH (Bubonic Plague)
Target: Protein-Tyrosine Phosphatase
What strain of Yersinia is this in and what is the NCBI gene #? - Dr .B
NCBI Gene # or RefSeq#:
EC#: 3.1.3.48
PDB # or closest PDB entry is using homology model:
2Y2F
Link -> http://www.pdb.org/pdb/explore/explore.do?structureId=2Y2F
Background/Disease:
During the 14th century, a disease known as the bubonic plague wiped out about one-third of the population in Europe. Classified as a zoonotic disease, it spread to the human population by small rodents and their fleas. Also known as the Black Death, the disease killed an infected individual within 4 days if left untreated. People with the disease experienced swollen lymph nodes (buboes), chills, high fever, muscle cramps, seizures, and change in skin color. The swollen lymph nodes were commonly found in the armpits, groin or neck, and were associated with pain. The cause of the bubonic plague was recently confirmed to the organism Yersinia pestis. It is a gram-negative bacteria that can take three main forms, the bubonic plague being the most prominent. Yersinia pestis attacks humans by using organisms like a flea as a vector. The bacteria accumulates inside the gut of a flea, and once the flea bites a human host, infected blood from the flea enters a human. The bacteria quickly spreads to the lymph nodes, infecting the lymphatic system. Phagocytes are not effective against Yersinia pestis because the bacteria can resist phagocytosis and kill them instead. As the disease progresses, lymph nodes can become necrotic and problems with the lungs can occur. Over 200 different rodents and species can also serve as hosts even though the flea is the most common. Although the disease is not extremely present in humans as it once was 7 centuries ago, cases of the plague are still reported to the World Health Organization.
Image of protein (PyMol or etc):
CDS Gene Sequence: 921 base pairs
1 ATGCGTGAACGTCCTCACACCAGCGGTCACCACGGTGCGGGTGAGGCGCGTGCGACGGCT
61 CCTTCTACCGTTTCTCCATACGGTCCGGAAGCCCGTGCGGAACTGAGCTCTCGTCTGACC
121 ACCCTGCGTAATACCCTGGCTCCGGCGACCAACGACCCGCGTTACCTCCAGGCGTGCGGT
181 GGTGAAAAACTGAACCGTTTTCGTGACATCCAGTGTCGTCGCCAGACTGCTGTACGCGCG
241 GACCTGAACGCGAACTATATCCAGGTCGGTAACACCCGTACCATCGCGTGCCAGTATCCG
301 CTGCAATCTCAACTGGAGTCTCACTTCCGTATGCTGGCCGAAAACCGCACCCCGGTGCTC
361 GCGGTTCTGGCGTCCTCCTCTGAAATCGCTAACCAGCGCTTTGGTATGCCGGACTACTTT
421 CGTCAATCTGGTACCTACGGCTCTATCACCGTTGAATCTAAGATGACCCAGCAAGTTGGC
481 CTGGGTGACGGTATCATGGCGGACATGTACACGCTGACCATCCGTGAAGCCGGTCAGAAA
541 ACCATCAGCGTCCCAGTGGTCCACGTTGGTAACTGGCCGGATCAGACCGCAGTTAGCAGC
601 GAGGTTACGAAAGCCCTCGCGTCTCTGGTTGACCAAACGGCGGAGACTAAACGTAACATG
661 TATGAAAGCAAAGGTTCTTCTGCGGTTGCGGACGACTCTAAACTGCGTCCTGTTATTCAC
721 TGCCGTGCCGGTGTAGGTCGTACCGCGCAGCTGATCGGTGCGATGTGCATGAACGATTCT
781 CGTAACAGCCAGCTGTCTGTCGAAGATATGGTTTCTCAGATGCGTGTTCAGCGTAATGGC
841 ATCATGGTTCAGAAAGACGAACAACTCGACGTACTCATCAAACTGGCGGAAGGTCAGGGT
901 CGTCCACTGCTGAACTCTTAA
OLIGOS (actual ones ordered from IDT DNA in 2011 - for Juan Carlos Salazar) - Dr. B Jan 12th, 2018
YopH_1 ATGCGTGAACGTCCTCACACCAGCGGTCACCACGGTGCGGGTGAGGCGCGTGCGACG
YopH_2 GTTCCGCACGGGCTTCCGGACCGTATGGAGAAACGGTAGAAGGAGCCGTCGCACGCGCCT
YopH_3 GAAGCCCGTGCGGAACTGAGCTCTCGTCTGACCACCCTGCGTAATACCCTGGCTCCGGCG
YopH_4 TCAGTTTTTCACCACCGCACGCCTGGAGGTAACGCGGGTCGTTGGTCGCCGGAGCCAGGG
YopH_5 TGCGGTGGTGAAAAACTGAACCGTTTTCGTGACATCCAGTGTCGTCGCCAGACTGCTGTA
YopH_6 GGTGTTACCGACCTGGATATAGTTCGCGTTCAGGTCCGCGCGTACAGCAGTCTGGCGACG
YopH_7 CTATATCCAGGTCGGTAACACCCGTACCATCGCGTGCCAGTATCCGCTGCAATCTCAACT
YopH_8 CCGGGGTGCGGTTTTCGGCCAGCATACGGAAGTGAGACTCCAGTTGAGATTGCAGCGGAT
YopH_9 GAAAACCGCACCCCGGTGCTCGCGGTTCTGGCGTCCTCCTCTGAAATCGCTAACCAGCGC
YopH_10 CCGTAGGTACCAGATTGACGAAAGTAGTCCGGCATACCAAAGCGCTGGTTAGCGATTTCA
YopH_11 CGTCAATCTGGTACCTACGGCTCTATCACCGTTGAATCTAAGATGACCCAGCAAGTTGGC
YopH_12 GATGGTCAGCGTGTACATGTCCGCCATGATACCGTCACCCAGGCCAACTTGCTGGGTCAT
YopH_13 ACATGTACACGCTGACCATCCGTGAAGCCGGTCAGAAAACCATCAGCGTCCCAGTGGTCC
YopH_14 AACCTCGCTGCTAACTGCGGTCTGATCCGGCCAGTTACCAACGTGGACCACTGGGACGCT
YopH_15 GCAGTTAGCAGCGAGGTTACGAAAGCCCTCGCGTCTCTGGTTGACCAAACGGCGGAGACT
YopH_16 CCGCAACCGCAGAAGAACCTTTGCTTTCATACATGTTACGTTTAGTCTCCGCCGTTTGGT
YopH_17 TTCTTCTGCGGTTGCGGACGACTCTAAACTGCGTCCTGTTATTCACTGCCGTGCCGGTGT
YopH_18 GAATCGTTCATGCACATCGCACCGATCAGCTGCGCGGTACGACCTACACCGGCACGGCAG
YopH_19 GCGATGTGCATGAACGATTCTCGTAACAGCCAGCTGTCTGTCGAAGATATGGTTTCTCAG
YopH_20 CTTTCTGAACCATGATGCCATTACGCTGAACACGCATCTGAGAAACCATATCTTCGACAG
YopH_21 ATGGCATCATGGTTCAGAAAGACGAACAACTCGACGTACTCATCAAACTGGCGGAAGGTC
YopH_22 TTAAGAGTTCAGCAGTGGACGACCCTGACCTTCCGCCAGTTTGAT
Amino Acid Sequence:
1 MRERPHTSGHHGAGEARATAPSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACG
61 GEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVL
121 AVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQK
181 TISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIH
241 CRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQG
301 RPLLNSX
Primers:
Forward:
TACTTCCAATCCATGCGTGAACGTCCTCACAC
32 bp long
@ xmM Mg2+
GC content: 50%
Reverse:
@ xmM Mg2+
Melting Temp
Expasy ProtParam Results:
Numbers of amino acids: 306 Molecular Weight: 33512.8 kDa Theoretical pI: 8.99